Just went through this myself and ended up with a 2003 which I repowered with Yamaha F250 Offshore (4.2L) with digital controls and also upgraded the electronics to a Garmin 7612xsv system!
The 330 from 2003 and before is only rated to 500HP on the transom. From 2004 to 2007 the rating is 600HP, and from 2008 onwards it's 700HP. (you may want to double check this with Grady!) There are a lot of differing opinions on whether one can or should exceed the manufacturer's HP rating (and if your insurance company will honor a claim on such a boat), but the main reason I went with the F250's is that I already owned a well maintained pair from my previous boat.
Also, surprisingly, Grady's own performance bulletins comparing the F250's and F300's did not show that big of an improvement. Here are the numbers below: (Grady has since removed the 500HP bulletin from their website because they are no longer offering the F250's as an option)
500HP (twin F250 4.2L Offshore)
Best Cruise: 30.7 MPH (4300 RPM), 1.17 mpg
5000 RPM: 36.9 MPH, 1.02 mpg
Max Speed: 42.9 MPH, .90 mpg
600HP (twin F300 4.2L Offshore)
Best Cruise: 29.9 MPH (4200 RPM), 1.25 mpg
5000 RPM: 37.1 MPH, 1.08 mpg
Max Speed: 44.6 MPH, .86 mpg
700HP (twin F350)
Best Cruise: 32.3 MPH (3900 RPM), 1.22 mpg
5000 RPM: 43 MPH, .95 mpg
Max Speed: 50.4 MPH, .75 mpg
As I really enjoy a fun refit project and I knew I would be repowering and redoing the electronics, I was pretty happy to find an older hull in great shape. I don't intend to sell the boat for many many years, so I wasn't worried about the potential resale value difference between F300's or F250's. I was, however, very focussed on only getting a boat that had the factory installed bow thruster and the Fischer Panda diesel genset.
Also if you end up needing to redo the dash, see this thread:
viewtopic.php?f=3&t=23367
Let us know what you end up getting!
Joe